ARCHIVED - How do we earn Faction Reputation?

If you recall, it was impossible to earn Reputation with New Monarchy, Dead Orbit, or Future War Cult in the Beta; though these factions would sometimes give you Side Missions while in Explore mode (received through beacons), completing these missions only rewarded you with Vanguard reputation, and occasionally 100 Glimmer.
Even playing in the Crucible did not earn you reputation; though the Control playlist was supposedly hosted by Dead Orbit, you did not earn any Dead Orbit reputation for playing it... only Crucible reputation.
Will this have changed in the final game? Or do we earn faction rep by some other means? The unique faction weapons & armor are purchased with Crucible Marks, you think we'd at least be able to earn faction rep in the Crucible.